I haven't watched it in a long time so I had to go back and watch a few minutes of the ending.
They have always had similar but different goals. He dreamed of helping the country and its people through the 'government' (monarchy) and she dreamed of helping people and leading the workers of her trading company. These are big goals and dreams they're both very serious about.
She never wanted a life in the palace at any point. He was reluctant to be ruler for a long time but you could slowly see it take over his character. He wanted to lead by the end of the show.
I'm sure she always knew in the back of her mind but it became obvious in the last episode: they have different paths. He can't run away and be with her. She can't live a life in the palace (she's not even his wife in the eyes of the country - his half-sister is his "official" wife). Most if not all of her happy moments with him are when they're alone or at her trading company and not at his home or at the palace. She wanted someone by her side, not to be at his side.
Sometimes dreams, goals, responsibilities and ambitions outweigh the desire to live with your love.
They promised to meet again. You get a scene showing he never forgets about her (with his longer beard to make him look older). And then you get that scene at the very end where they meet again.
I took it as she had died (she had lots of health problems and I doubt that bath in the ice-lake fixed everything) and was waiting for him. And he shows up.
They couldn't have a happily ever after in their lives but in their next life or afterlife they do.